Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate GFF2918 PS417_14930 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__WCS417:GFF2918 Length = 387 Score = 152 bits (384), Expect = 2e-41 Identities = 115/362 (31%), Positives = 177/362 (48%), Gaps = 23/362 (6%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60 M+ N ++E A R+ VR + A R+ I+ E V + L GW Sbjct: 1 MNPNDNEELNAIREGVRALCAEFDAAYWRR--IDEEKGFPEAFV---KALTDAGWLSAMI 55 Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120 P+ YGG+G + + EE+ G + GSE QK+ +LP++A+ Sbjct: 56 PEAYGGSGLGLAEASVILEEVNRCGGNSGTVHGQMYNMFTLLRHGSEAQKRLYLPKLASG 115 Query: 121 D-DWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAA 179 + G +EP +G+D +KT A K+GDK++INGQK W + QH+D + L RT P A Sbjct: 116 ELRLQSMGVTEPSTGTDTTKIKTTAIKRGDKYVINGQKVWISRVQHSDLMILLARTTPLA 175 Query: 180 ---KKQEGISFILVDMKT---KGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKG 233 KK EG+S LVD++ G+TV+PI + HE NE+FFD++E+PL++L+G+E KG Sbjct: 176 EVKKKSEGMSIFLVDLREAIGNGLTVQPIANM-VNHETNELFFDNLELPLDSLIGEEGKG 234 Query: 234 WDYAKFLLGNERTGIAR--VGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIE 291 + Y L ERT IA +G + I + A G+P+ ++ + +A IE Sbjct: 235 FKYILDGLNAERTLIAAECIGDGRWFIEKASAYARDRVVFGRPIGQNQGVQFPIAEAHIE 294 Query: 292 LKALELTQLRVVA--DEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIG--PFAAPY 347 ++A +L + R D GK N A K ++ ++ G FA Y Sbjct: 295 IEAADLMRWRACEEYDSGKQAGASANMA----KYLAAKASWEAANACLQTHGGFGFACEY 350 Query: 348 DV 349 DV Sbjct: 351 DV 352 Lambda K H 0.317 0.135 0.411 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 360 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 396 Length of database: 387 Length adjustment: 31 Effective length of query: 365 Effective length of database: 356 Effective search space: 129940 Effective search space used: 129940 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory